The brain, a marvel of complexity, houses an array of neurons, each with its unique shape and electrical behavior. This diversity, both within and across cell types, forms the basis of the brain’s cognitive abilities. A new Blue Brain study, published in iScience, takes a bold leap into the realm of detailed biophysical neuron models, steering away from oversimplified representations. The focus here is on unraveling the intricate interplay between morphology (shape) and electrophysiology (behavior), and understanding and reproducing the variability observed in experimental data.
Detailed single neuron modeling has emerged as a powerful tool for exploring the intricacies of neuronal function. However, the diversity of neurons in the mammalian cortex, the outer layer of the brain responsible for higher cognitive functions, poses a significant challenge, as existing computational tools often focus on specific features of a single neuron type. In this new study, appearing on the cover of November’s Patterns, the EPFL Blue Brain Project introduces a groundbreaking new universal workflow that simplifies the creation, validation, and generalization of detailed neuronal models, offering researchers unprecedented insight into the world of neural science. Its usefulness and performance are demonstrated by the building of cell models for a significant portion of the rat cortex.
In conjunction with the recent release of preprints on the modeling of the rat Somatosensory Cortex, the brain’s center for processing sensory information, EPFL’s Blue Brain Project has open sourced important software packages for simulation neuroscience. It is hoped that access to these new tools will help neuroscientists make the most of the large amounts of data as well as the related open source model which BBP researchers have shared at the same time.
Scientists at EPFL’s Blue Brain Project have developed a groundbreaking computational model of the thalamic microcircuit in the mouse brain, offering new insights into the role this region plays in brain function and dysfunction.
This research topic, published in Frontiers in Neuroinformatics, represents an update on the state of neuroscientific software, assesses the impact of the increased computational capabilities on scientific questions, and gives an outlook on future opportunities and challenges of computational neuroscience.
It is well established that the shape of nerve cells, such as neurons and glial cells, can have a big impact on their functioning. Accurate structural models can help to shed more light on the relation between structure and function; more realistic structural models allow researchers to further zoom in on this question. In a new publication in Briefings in Bioinformatics, scientists from the EPFL Blue Brain Project working with an international team of scientists share a new neuroscience-dedicated framework, Ultraliser, capable of building these structural models with realistic and detailed cellular geometries that can be used in in silico neuroscience research. The software is available as open source.
The brain is made up of billions of neurons that communicate with each other by forming trillions of synapses. Transmission between these synapses is the primary method of communication between neurons and has been extensively studied in rodents. However, far less is known about synaptic transmission in the human brain. An exciting new study in a front cover paper published in Cerebral Cortex, set out to quantitatively characterize a selected neural pathway in the human neocortex.
A new study published in the journal GLIA has found that targeting astrocytes, which are cells that play crucial functions within neuronal circuits, may be an effective strategy in preventing the decline of neurons in Alzheimer’s disease (AD). The study, conducted by teams of researchers from the University of Lausanne and EPFL’s Blue Brain Project, found that overexpressing a specific protein in the astrocytes prevented many of the neurological changes seen in AD mice model and helped in preserving short term memory.
After four years of research, EPFL’s Blue Brain Project shares an enriched version of their 3D digital cell atlas of the mouse brain which includes more neuron types. The new approach can be extended to any other cell type, and provides a resource to build tissue-level models of the mouse brain.
Modern day science typically involves iterative cycles of data discovery, acquisition, preparation, analysis, model building and validation which often lead to knowledge discovery as well as knowledge sharing and dissemination. Given the ambitious goal of digitally building and simulating the mouse brain, the EPFL Blue Brain Project required a data and knowledge management system that could not only handle the enormous diversity and evolution of data at the scale of the whole brain, but also track the data’s provenance to ensure quality, reproducibility and accurate attribution throughout these iterative cycles. Accordingly, Blue Brain built and open sourced Blue Brain Nexus as a key technology for organizing brain tissue data and models and as a complementary approach to classical neuroinformatics tools. Blue Brain Nexus has now grown into an ecosystem of secured, domain-agnostic, scalable and interoperable tools with a growing community of adopters including large international organizations, across use cases that include neuroscience, psychiatry and open linked data.
Understanding the functional aspects of our brain implies understanding the structure-function relationship of billions of individual interconnected neurons; a particularly convoluted problem as the structure of each neuron affects the whole network and its dynamics. Neurons have visually complex structures, multiple classes of shapes (morphologies) and electrophysiological classifications, making them complicated computational objects to study. Accurate visualization of simulation results depend on highly accurate “3D surface” (mesh) models, where each component can be mapped; however the generation of such models is challenging. Here, the EPFL Blue Brain Project presents a simple and effective method to create mesh models of spiny neurons (neurons with small spikes along their surface) from their corresponding morphologies.
Simulating neurons down to the level of their biochemistry in order to understand their behavior and properties is a complex computational challenge. While small to the human eye, a neuron is a comparatively large object relative to its biochemical constituents. Yet, the overall behavior of a neuron depends on the specific composition and interactions at the molecular level that will control its electrical properties. It’s like aiming to fully describe a patch of forest down to the millimeter, recording the location and shape not only of each tree and each leaf, but of each grain of dirt.
Even with high performance computing and ever increasing computing power, scientists still have to make uncomfortable compromises; phenomena that are random in nature are averaged out for ease of calculation, or only parts of a cell can be described with molecules and their interactions. Needing to choose between what is biologically relevant and what is able to be addressed, leads to significant loss of information and, often, relevance.
Now, teams from the EPFL Blue Brain Project and from the Okinawa Institute of Science and Technology Graduate University, Japan (OIST) describe how they pushed the boundaries of simulating biochemical diffusion-reaction models to the scale of entire neurons. The new solution dramatically reduces the computer memory needed while maintaining similar or better performance, increasing overall scalability.
In the Spring of 2022, the EPFL Blue Brain Project announced in a paper published in Cell Reports that it had found a way to mathematically build the 3D tree-like geometries of neurons using algebraic topology. One of the main branches of pure mathematics, algebraic topology allowed Blue Brain to describe the geometrical shapes of neurons in a way that could be used to build their digital twins. This breakthrough opens the path to using computers to automatically build digital copies of any of the thousands of different types of neurons found in the brain. The study, led by Blue Brain’s Neuromathematics Leader Lida Kanari and EPFL Professor Kathryn Hess of the Laboratory for Topology and Neuroscience, was the latest in a series of Blue Brain studies where algebraic topology helped tackle and solve a wide range of previously intractable neuroscience problems.
As the study of neuroscience accelerates ever faster and our understanding of the intricate workings of the brain deepens, the need to define a standardized approach to naming neuron types has become imperative. As the building blocks of the brain, neurons are studied intensely with vast amounts of data being generated and shared. With this comes several challenges as there is more and more data to describe different cell types. Furthermore, the literature contains many neuron names that are commonly used and accepted, even when it is unclear how such common usage types relate to the many proposed evidence-based types that are based on the results of new techniques. In addition, there is the significant question of comparing different data sets across labs. This all points to an urgent need for a standardized approach to naming neurons and for the organization of knowledge about their properties.
The EPFL Blue Brain Project will be featuring in the exciting Brain(s) exhibition at the Barcelona Centre of Contemporary Culture starting this month and later in the year at the Fundación Telefónica Madrid.
Throughout evolution, individual cells have been making successful decisions on their own, even while forming parts of vast networks, such as neurons and glia in the human brain. Now scientists from the EPFL Blue Brain Project and King Abdullah University of Science and Technology (KAUST) have published a new theory describing a secret language that cells may use for internal dialog about the external world.
Using a computational model, they hypothesize that metabolic pathways, which are primarily a means of extracting energy and building block molecules from glucose and other substrates to feed the brain, might also be capable of coding details about neuromodulators that stimulate increases in energy consumption. If true, this would open the door to a nearly infinite number of possibilities for information processing in nervous systems as component cells could compute in previously unexplored ways. Such a mechanism would also help explain the remarkable energy efficiency of brains.
In recent years, simulation alongside theory and experimentation, has firmly become the third pillar for studying the brain. The computational models of brain components, brain tissue or even whole brains provide new ways to integrate anatomical and physiological data and allow insights into causal mechanisms crossing scales and linking structure to function.
What underlies learning in the brain might be actually simpler than previously thought despite the brain being one of the most complex objects in the known universe. A collaboration of Scientists led by the EPFL Blue Brain Project has achieved a major advance in accurately simulating the synaptic changes thought to implement learning in the neocortex, opening the door to greater understanding of learning in the brain.
EPFL’s Blue Brain Project has found a way to use only mathematics to automatically draw neurons in 3D, meaning we are getting closer to being able to build digital twins of brains.
The messages sent between neurons look something like a Morse code, but the closer one looks the more mysterious the code becomes. The code is called the neural code and is the holy grail in neuroscience because if this code is cracked, then one could simply intercept the messages and
decode what the brain is seeing, feeling, and thinking. Theories have fallen from grace one after another for over a century. But now researchers may have uncovered that the mystery may come from the way that time is used to represent information in the brain.
The hippocampus is a major component of the mammalian brain, which contributes to important cognitive functions such as memory consolidation and recall, and spatial navigation. The EPFL Blue Brain Project has launched a brand new Massive Open Online Course (MOOC) to enable students to learn how to simulate a Hippocampus Microcircuit and learn more about this fascinating brain region.
Living with the effects of the SARS-CoV-2 virus (COVID-19) for nearly two years, we have all come to understand the importance and role of diagnostic testing in responding effectively to the immense threat of COVID-19. Back in early 2020, the EPFL Blue Brain Project and FIND, the global alliance for diagnostics, collaborated to develop a Diagnostic Implementation Simulator for SARS-CoV-2 diagnostics, which uses modelling data to simulate scenarios and estimate the potential impact of deploying different testing strategies for COVID-19. The collaboration has today released an updated version of the Simulator, which has evolved to keep pace with the specific needs of COVID-19 and address public health requirements. The Simulator is now capable of modelling specific testing scenarios and multiple pandemic phases.
Blue Brain has created the first digital reconstruction of the Neuro-Glia-Vascular (NGV) Architecture providing a new framework to study brain function in health and disease.
The study, published in Cerebral Cortex, represents a major milestone for the EPFL Blue Brain Project because they can now reconstruct the architecture of non-neuronal entities such as blood vessels and the supporting cells called glia. This means it is possible to capture the way that neurons, glia and the blood supply interact. These reconstructions of the brain tissue provide a sub-micron precise framework needed to simulate the molecular interactions relevant to understanding how neurons are supported and nurtured. They can also be used to investigate how drugs interact and explore how neurodegenerative diseases arise. Blue Brain has made all the experimental data, models and tools used to reconstruct brain tissue at this resolution, open source in the Blue Brain NGV web portal.
Blue Brain open sources a simulation-ready database to accelerate molecular and systems biology.
Atlases of the brain are an essential tool for neuroscientific research as they make it possible to see diverse and multimodal data in the same reference frame. This is particularly the case for the EPFL Blue Brain Project where our work requires the acquisition and integration of high quality maps of data of the rodent brain. As those data sets are acquired from different animals, the integration thereof requires a registration step, i.e. bringing individual datasets in spatial overlap.
Voltage-sensitive dye imaging (VSDI) is a potentially powerful technique to track the electrical activity of thousands of neurons in the brain. However, the light signals generated when light interacts with dyes that are applied to the brain is so complex that it has been difficult to develop the full potential of this technique. In particular, it has been challenging to separate the thousands of light pulses coming from each neuron. To solve this problem, Blue Brain researchers simulated light traveling through a model brain and interacting with dye molecules. They could see, for the first time, how thousands of neurons work in groups.
Why do some people get sick and die from COVID-19 while others seem to be completely unaffected?
EPFL’s Blue Brain Project deployed its powerful brain simulation technology and expertise in cellular and molecular biology to try and answer this question. A group in the Blue Brain assembled an AI tool that could read hundreds of thousands of scientific papers, extract the knowledge and assemble the answer – A machine-generated view of the role of Blood Glucose Levels in the severity of COVID-19 was published today by Frontiers in Public Health.
The Blue Brain Project follows a four-year roadmap with specific scientific milestones to achieve its ultimate goal, digitally reconstructing and simulating the entire mouse brain. One of the goals in the current period is to model structures with direct relevance for the neocortex. The thalamus is highly interconnected with the cortex and plays an important role in an array of cognitive processes. It funnels sensory input to the neocortex with the thalamocortical loop playing a central role in cerebral rhythmogenesis (biological rhythm). As such, it has a key role in many functions, such as sleep and wakefulness and is involved in various diseases associated with dysfunction of rhythmic activity such as epilepsy, autism, schizophrenia and bipolar disorder. However, there is much that scientists do not know about this brain region and as the understanding of the thalamocortical system deepens, so does the complexity of the questions scientists face.
Recognizing the importance of understanding the structural and biochemical basis of astrocyte-mediated neuronal energy metabolism in the mammalian brain, the King Abdullah University of Science and Technology (KAUST) and EPFL Blue Brain Project Alliance was set up in 2013 to focus on this area of brain research.
When the full-scale effect of the COVID-19 pandemic was starting to be understood in early 2020, the EPFL Blue Brain Project and ETH Zurich, as part of the Swiss National COVID-19 Science Task Force, began collaborating with Spiez Laboratory on an online Platform – Academic Resources for COVID-19 (ARC). In a paper published in Frontiers for Public Health, the authors explain how the ARC Platform was set up to be a service to support Swiss diagnostic laboratories that are testing for SARS-CoV-2. The ARC Platform matched requests for critical equipment, reagents and consumable goods required by Swiss diagnostic laboratories involved in combating COVID-19 with supplies available from Swiss academic groups. Since then, with further input from Swiss startup Apptitude SA, the Platform has evolved with the needs of the epidemiological situation and the technology has been open sourced with the purpose to serve public health as a response solution for other countries and communities in the current COVID-19 crisis or in future crises.
The rodent Hippocampal formation is one of the most exhaustively studied regions in the mammalian brain but until now, there has not been a comprehensive knowledge base of its synaptic physiology. In a front cover paper published in the journal Hippocampus, researchers at EPFL’s Blue Brain Project present a data-driven approach to integrate the current knowledge on the hippocampal CA1 region using an open-access, comprehensive resource.
With the EPFL Blue Brain Project’s determination to make our computing resources and expertise available for the fight against COVID-19, we brought our experience in software development to team up with the Foundation for Innovative New Diagnostics (FIND). FIND is a global non-profit organization focused on diagnostics, currently co-convening the Access to COVID-19 Tools (ACT) Accelerator Diagnostics Partnership alongside The Global Fund, as a key part of the global response to the pandemic.
According to the World Health Organization (WHO), diagnostic testing for COVID-19 is critical to tracking SARS-CoV-2 (the virus responsible for COVID-19), understanding epidemiology, informing case management, and suppressing transmission. With diagnostics emerging as one of the most pressing issues in the COVID-19 crisis, Blue Brain has collaborated with FIND to develop a Diagnostic Implementation Simulator for SARS-CoV-2 diagnostics.
A deluge in digital data, the trend for cross-disciplinary and multi-modal scientific investigations along with the tremendous computing power now available, has led to team based, data-driven and data-intensive methods commonly used in science. These advances also come with a set of challenges summarized in the FAIR (1) guiding principles for research data management – make heterogeneous data generated from different contexts, Findable, Accessible, Interoperable and Reusable. Accordingly, Knowledge Graphs have become the go-to key solution across both research and industry to address these challenges.
The increase in the availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in the scale, complexity, and biological realism of computational models in neuroscience. Accordingly, to support construction and simulation, as well as the sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary.
With Switzerland starting to transition out of lockdown, testing for SARS-CoV-2, being a cornerstone of all response strategies, is more important than ever in order to contain the risk of a renewed increase in cases as public life slowly picks up again. Ensuring an adequate number of daily tests for this task requires precise and timely distribution of equipment, supplies and other resources. To support this endeavor, the EPFL Blue Brain Project and ETH Zurich, as part of the National COVID-19 Science Task Force, are collaborating with Spiez Laboratory on an online platform, Academic Resources for COVID-19 (ARC), to match critical support needed by Switzerland’s diagnostic laboratories with the support offered by the Swiss academic sector.
The EPFL Blue Brain Project will be featuring in the ‘Neurons, Simulated Intelligence’ exhibition at the Centre Pompidou in Paris, 26 Feb – 20 Apr 2020.
For the first time, scientists at the EPFL Blue Brain Project, a Swiss brain research initiative, have extended performance modelling techniques to the field of computational brain science resulting in findings that are useful for today and indispensable for the future. In a paper published in Neuroinformatics, they provide a quantitative appraisal of the performance landscape of brain tissue simulations, and analyze in detail the relationship between an in silico experiment, the underlying neuron and connectivity model, the simulation algorithm and the hardware platform being used. Thereby deriving the first analytical performance models of detailed brain tissue simulations, which is a concrete step to enable the next generation of brain tissue simulations.
Detailed neuron models consisting of thousands of synapses are key for understanding the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these models are however, computationally expensive (using lots of computing hours), which considerably decreases their utility. For the first time, Scientists at the Hebrew University of Jerusalem and the EPFL Blue Brain Project have formulated a unique analytical approach to the challenge of reducing the complexity of neuron models while retaining their key input/output functions and their computational capabilities. ‘Neuron_Reduce’ is a new computational tool that provides the scientific community with a straightforward capability to simplify complex neuron models of any cell type and still faithfully preserve its input-output properties while significantly reducing simulation run-time.
In order to improve performance and benefit from new computing architectures the EPFL Blue Brain Project has isolated the core functionalities of the NEURON simulator and optimized them into a new simulator engine CoreNEURON. In a paper published in Frontiers in Neuroinformatics, the Blue Brain explains how CoreNEURON helps existing NEURON users to simulate their models faster, better utilize computing resources and ultimately help to deliver science sooner.
Tooth decay (dental caries) is a major global public health problem and according to the WHO is the most widespread non-transmissible disease in the world. Transillumination with near-infrared light imaging (TI) has been shown to be effective in the vital early detection of tooth decay. Applying translational research and technology, scientists from the EPFL Blue Brain Project and the University of Geneva have collaborated to develop a new deep learning model for the automated detection and localization of dental lesions in TI images.
Researchers at EPFL’s Blue Brain Project, a Swiss brain research Initiative have combined two high profile, large-scale datasets to produce something completely new –a first draft model of the rules guiding neuron-to-neuron connectivity of a whole mouse neocortex. Based on these rules, they were able to generate statistical instances of the micro-connectome of 10 million neurons, a model spanning five orders of magnitude and containing 88 billion synaptic connections that will serve as the basis of the world’s largest-scale simulations of detailed neural circuits.
How does the brain find order amidst a sea of noise and chaos? Researchers at the EPFL Blue Brain Project have found the answer to this long-standing question by using advanced simulation techniques to investigate the way neurons talk to each other while submerged in a sea of noise and chaos. In a paper published in Nature Communications, they found that by working as a team, cortical neurons can respond even to weak input against the backdrop of noise and chaos, allowing the brain to find order.
The Blue Brain Project’s ‘Channelpedia’ is open to brain modellers and pharmacologists everywhere.
Pores at the surface of neurons and muscle cells control your every thought, movement; the very beating of your heart. The way the pores behave – that is open, close, or lock for a short time (inactivate) depending on voltage – shapes signals in the form of electrical charge (ions) moving across the cell surface.
For the first time, researchers at the EPFL’s Blue Brain Project have mapped the behavior of the largest family of these voltage-gated ion channels: Kv channels.
Published in Frontiers in Cellular Neuroscience, with freely available online data, their pioneering work will power virtual drug discovery – and, they hope, the first whole-brain simulation.
The EPFL Blue Brain Project has built the first next-generation models of thalamocortical neurons. These digital models of thalamocortical neurons were built using state-of-the art optimization techniques, which directly constrain unknown parameter values with experimental data. Thalamocortical neurons are essential components in the transmission of information from the outside world to higher order brain areas, such as the neocortex. These neurons fire action potentials in distinct modes, which are associated with different brain states, such as wakefulness and sleep. These findings are the first phase towards the complete modelling of the rodent thalamus, which is the next step for the Blue Brain Project. In addition, the experimental and modelling community can now use these data and models in their analysis and modelling workflows.
How do neurons process information? Neurons are known to break down an incoming electrical signal into sub-units. Now, researchers at Blue Brain have discovered that dendrites, the neuron’s tree-like receptors, work together – dynamically and depending on the workload – for learning. The findings further our understanding of how we think and may inspire new algorithms for artificial intelligence.
EPFL’s Blue Brain Project has open sourced NeuroMorphoVis, an interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks.
Second Neuromodulation of Neural Microcircuits NM² Conference encourages further momentum in the bid to understand the mechanisms and principles of neuromodulation
The EPFL Blue Brain Project was delighted to be invited as a speaker at the Congress of the Swiss Foundation for Educational Media 2019 (Fondation Suisse pour la Formation par l’Audiovisuel, FSFA)
In a front-cover paper published in Cerebral Cortex, EPFL’s Blue Brain Project, a Swiss Brain Research Initiative, explains how the shapes of neurons can be classified using mathematical methods from the field of algebraic topology. Neuroscientists can now start building a formal catalogue for all the types of cells in the brain. Onto this catalogue of cells, they can systematically map the function and role in disease of each type of neuron in the brain.
The Blue Brain Project is delighted to announce that it will be hosting in May this year, the second Neuromodulation of Neural Microcircuits NM² Conference.
Blue Brain’s Cristina Colangelo wins Best Flash Talk at the first Swiss Early-Career Researchers Symposium
The first digital 3D atlas of every cell in the mouse brain provides neuroscientists with previously unavailable information on major cell types, numbers and positions in all 737 brain regions – which will potentially accelerate progress in brain science massively. Released by EPFL’s Blue Brain Project and published in Frontiers in Neuroinformatics, the Blue Brain Cell Atlas integrates data from thousands of whole brain tissue stains into a comprehensive, interactive and dynamic online resource that can continuously be updated with new findings.
The Blue Brain Project will be part of the Nomads Foundation exhibition ‘Futur des métiers’ at the Cité des Métiers taking place in the Palexpo Exhibition Centre, Geneva, Switzerland this November.
The EPFL Blue Brain Project recently welcomed a delegation of primary and secondary school heads and Neurology students from Slovenia to the Campus Biotech.
The Blue Brain Project was delighted to receive a visit from 56 students with a strong interest in science, from India as part of their trip to Switzerland organized by the Life Lab Foundation.
This course explores the latest data, models, and techniques for investigating the different levels of the brain. Find new insights and derive new theories.
The Blue Brain Project is delighted to be taking part in ‘Planète Santé Live’ at the Palexpo Exhibition Centre, Geneva, Switzerland. October 4-7, 2018.
Originally, one of Blue Brain’s first domain specific interactive visualization tools, the latest version of RTNeuron provides a scalable real-time rendering tool for the visualization of detailed neuronal simulations based on cable models. This allows the visualization of neurons, synapses and playback of simulation data as well as other basic geometrical objects.
Blue Brain was delighted to welcome the New York Times Student Journeys groups for a visit to the Project. The New York Times Student Journeys offers educational travel programs for high school students and Blue Brain is part of the itinerary during their three-week visit to Switzerland.
EPFL Blue Brain Project deploys its next supercomputer – Blue Brain 5
Hewlett Packard Enterprise (HPE) today announced that the Ecole Polytechnique Fédérale de Lausanne’s (EPFL) Blue Brain Project, a Swiss brain research initiative, selected HPE to build a next-generation supercomputer for modeling and simulation of the mammalian brain. The new supercomputer, called ‘Blue Brain 5’, will be dedicated to simulation neuroscience, in particular simulation-based research, analysis and visualization, to advance the understanding of the brain.
Click here to read the HPE announcement.
Blue Brain is delighted to be a supporting partner as the SIB Swiss Institute of Bioinformatics celebrate its 20-year anniversary.
Frontiers hosted its second Data Services Workshop in Brussels on April 24 with this year’s workshop focusing on the application of open research data to support sustainable health initiatives. Drawing lessons from recent successes in the use of big data and artificial intelligence in data-intensive health research, it aimed to discuss policy challenges and actions necessary in Europe to unleash the full potential of open research data in health for the benefit of society.
Blue Brain’s Operations Director Adriana Salvatore presented the Blue Brain Project to a group of 100 MBA students from the IMD Business School with a specific focus on the operational side of the project.
Knowledge sharing is an important driving force behind scientific progress. In an open-science approach, EPFL’s Blue Brain Project has created and open sourced Blue Brain Nexus that allows the building of data integration platforms. Blue Brain Nexus enables data-driven science through searching, integrating and tracking large-scale data and models.
Simulating Biophysical Principles of Functional Synaptic Plasticity in the Neocortex – INCITE grant renewed for 2018
A team of scientists led by Eilif Muller of the Blue Brain Project, have had their INCITE grant renewed for 2018 to provide a further 160 million core hours at the Argonne National Laboratory. INCITE supports computationally intensive, large-scale research projects with large amounts of dedicated time on supercomputers at DOE’s Leadership Computing Facilities. In 2017, INCITE awarded the Blue Brain with 100 million core hours to simulate biophysical synaptic plasticity in reconstructions of the neocortical microcircuit to discover their synergistic functional principles.
During our lifetimes, our brains undergo continuous changes as a consequence of our experiences. Synaptic plasticity—the biological process by which brain activity leads to changes in synaptic connections, is thought to be central to learning and memory. However, little is known about how this process shapes biological neural networks.
With this renewed grant, the team that also includes scientists from the École polytechnique fédérale de Lausanne and The Hebrew University of Jerusalem will continue to focus on advancing our understanding of these fundamental mechanisms of the brain’s neocortex. The team is carrying out large-scale simulations of recently uncovered biophysical principles underlying synaptic plasticity in reconstructions of a neocortical microcircuit (Markram et al., 2015; 10.1016/j.cell.2015.09.029) consisting of around 200,000 neurons and 260 million synapses. The aim is to shed light on the synergistic functional principles that shape plasticity in realistic cortical circuits.
The team is also using DOE supercomputers to characterize: (1) the role of NMDA receptor spikes in plasticity induction; (2) the dynamics of neuronal assembly formation and maintenance; and (3) the computational impact of synaptic plasticity in common signal processing tasks. In addition to improving our understanding of the brain, this research could help inform the development of enhanced deep learning methods, as well as new learning paradigms for neuromorphic hardware.
Register for the MOOC: Simulation Neuroscience – reconstruction of a single neuron A unique, massive open online course taught by a multi-disciplinary team of world-renowned scientists
Simulation Neuroscience is an emerging approach to integrate the knowledge dispersed throughout the field of neuroscience.
The aim is to build a unified empirical picture of the brain, to study the biological mechanisms of brain function, behaviour and disease. This is achieved by integrating diverse data sources across the various scales of experimental neuroscience, from molecular to clinical, into computer simulations.
In this first course, you will gain the knowledge and skills needed to create simulations of biological neurons and synapses.
This course is part of a series of three courses, where you will learn to use state-of-the-art modeling tools of the Human Brain Project Brain Simulation Platform to simulate neurons, build neural networks, and perform your own simulation experiments. We invite you to join us and share in our passion to reconstruct, simulate and understand the brain!
What you’ll learn
- Discuss the different types of data for simulation neuroscience
- How to collect, annotate and register different types of neuroscience data
- Describe the simulation neuroscience strategies
- Categorize different classification features of neurons
- List different characteristics of synapses and behavioural aspects
- Model a neuron with all its parts (soma, dendrites, axon, synaps) and its behavior
- Use experimental data on neuronal activity to constrain a model
Meet the instructors:
Henry Markram – Professor EPFL, Founder and Director of the Blue Brain Project
Idan Segev – David & Inez Myers Professor in Computational Neuroscience at Hebrew University Jerusalem, and Adjunct Professor EPFL.
Sean Hill – Adjunct Professor EPFL, Blue Brain Project, Director of the Krembil Centre of Neuroinformatics at the Centre of Addiction and Mental Health in Toronto, Canada
Dr. Felix Schürmann – Adjunct Professor EPFL, Director Blue Brain Project
Dr. Eilif Muller – Section Manager, Cells & Circuits, Simulation Neuroscience, Blue Brain Project
Dr. Srikanth Ramaswamy – Senior Scientist, Cells & Circuits, Simulation Neuroscience, Blue Brain Project
Werner Van Geit – Systems Specialist, Neuroscientific Software Engineering, Computing, Blue Brain Project
Samuel Kerrien – Section Manager, Neuroinformatics Software Engineering, Computing, Blue Brain Project
Lida Kanari – PhD Student, Molecular Systems, Simulation Neuroscience, Blue Brain Project
The course is targeted at senior bachelor, master or PhD students in science or engineering fields looking for an introduction to Simulation Neuroscience.
It is a six-week course, with an estimated course load of 5-7 hours per week.
- Knowledge of ordinary differential equations, and their numerical solution
- Knowledge of programming in one of Python (preferred), C/C++, Java, MATLAB, R
Successful Neuromodulation of Neural Microcircuits NM² Conference prompts future collaborations
At the end of September, the Blue Brain Project concluded a stimulating, interactive and highly collaborative Neuromodulation of Neural Microcircuits NM² Conference. A global line-up of renowned speakers and more than one hundred attendees from across the different Neuromodulation communities ensured a cross-pollination of experience and expertise throughout the three-day Conference.
Neuromodulators – the master switches – dynamically reconfigure neural microcircuits and shape brain states by controlling the function of neurons and glia, dendrites, and synapses. Recently, the Blue Brain Project discovered that neocortical microcircuit activity shifts from synchronous to asynchronous network states that is tightly controlled by neuronal and synaptic physiology. This effect is strikingly similar to the function of neuromodulators, which control neurons and synapses to sculpt the emergence of brain states.
Therefore, understanding the mechanisms by which neuromodulators operate is not only fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, but also the global neuroscience community. Over the three days of the Conference, 34 leading experts in this field presented their current research and enthusiastically participated in panel discussions, as both speakers and participants took part in shaping the future course of neuromodulatory research. Srikanth Ramaswamy, NM² Conference Host said “This meeting is unique in that it focuses on the mechanisms by which diverse neuromodulators could give rise to similar behavioral states by differentially controlling neuronal and synaptic activity.”
With a strategic focus on the neuromodulation of microcircuits, the Conference provided a platform to identify common principles by which different neuromodulators regulate the activity of neurons and glia, dendrites, and synapses. Speaker and day three Chair Randy Bruno said “Biologists have been listening to the raucous activity of neural circuits for a century. Only recently have we begun to appreciate how neuromodulation quietly orchestrates it all”.
The successful NM2 Conference has not only provided a springboard to shape a follow-up event in 2019, but has also laid the foundation towards an international consortium to drive collaborative research in neuromodulation.
A Topological Representation of Branching Neuronal Morphologies
In a paper published in the journal Neuroinformatics, a team of scientists led by the Blue Brain Project, in collaboration with the Laboratory for Topology and Neuroscience, explain how the invention of the Topological Morphology Descriptor (TMD), provides a method for encoding the spatial structure of any tree as a “barcode”, a unique topological signature.
Many biological systems consist of branching structures that exhibit a wide variety of shapes. Understanding of their systematic roles is hampered from the start by the lack of a fundamental means of standardizing the description of complex branching patterns, such as those of neuronal trees.
As opposed to traditional morphometrics, the TMD couples the topology of the branches with their spatial extents by tracking their topological evolution in 3-dimensional space. The team prove that neuronal trees, as well as stochastically generated trees, can be accurately categorized based on their TMD profiles.
The TMD retains sufficient global and local information to create an unbiased benchmark test for their categorization and is able to quantify and characterize the structural differences between distinct morphological groups. The use of this mathematically rigorous method will advance our understanding of the anatomy and diversity of branching morphologies.
Click here to read the paper.
Comprehensive Morpho-Electrotonic Analysis Shows two Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex
The group of Idan Segev of the Hebrew University of Jerusalem and Christiaan P.J. de Kock of the Vrije Universiteit, Amsterdam, in collaboration with the Molecular Systems Section in the Simulation Neuroscience Division of the Blue Brain Project, employed feature-based statistical methods, on a rare data set of 60 3D reconstructed pyramidal neurons from L2 and L3 in the human temporal cortex (HL2/L3 PCs) removed after brain surgery.
Of these cells, 25 neurons were also characterized physiologically. Thirty-two morphological features were analyzed, 18 of which showed a significant gradual increase with depth from the pia (e.g., dendritic length and soma radius). The other features showed weak or no correlation with depth (e.g., dendritic diameter).
The basal dendritic terminals in HL2/L3 PCs are particularly elongated, enabling multiple nonlinear processing units in these dendrites. Unlike the morphological features, the active biophysical features (e.g., spike shapes and rates) and passive/cable features (e.g., somatic input resistance, membrane time constant, and dendritic cable length) appear to be depth-independent.
A novel topological descriptor for apical dendrites yielded two distinct classes, termed hereby as “slim-tufted” and “profuse-tufted” HL2/L3 PCs. The two classes also differ in their electrical properties, as the “profuse-tufted” cells tend to fire at higher rates. Therefore, two distinct morpho-electrotonic classes of HL2/L3 Pcs were identified for the first time.
Click here to read the paper published in Cerebral Cortex.
The Blue Brain Project launches three-day conference to kick-start neuromodulation research – NM2
- NM² Conference to address understanding the mechanisms by which neuromodulators operate which is both fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, and for the global neuroscience community
- Leading experts from around the world and EPFL to present and take part in panel discussions across the three days
- NM2² Conference to provide a unique platform for students and junior researchers to interact with leaders in the field to collectively take part in shaping the future course of neuromodulatory research
The Blue Brain Project is delighted to announce that it will be hosting a three-day conference – Neuromodulation of Neural Microcircuits NM² from September 18th to 20th, 2017.
Neuromodulators – the master switches – dynamically reconfigure neural microcircuits and shape brain states by controlling the function of neurons and glia, dendrites, and synapses. Recently, the Blue Brain Project discovered that neocortical microcircuit activity shifts from synchronous to asynchronous network states that is tightly controlled by neuronal and synaptic physiology. This effect is strikingly similar to the function of neuromodulators, which control neurons and synapses to sculpt the emergence of brain states. Therefore, understanding the mechanisms by which neuromodulators operate is not only fundamental to Blue Brain’s pioneering work in simulating brain function and dysfunction, but also the global neuroscience community.
The Conference will bring together world-leading experts to:
- Identify the state-of-the-art mechanisms of the neuromodulation of neural microcircuits
- Illuminate various strategies enabling the measurement of neuromodulatory states in brain health and disease
- Integrate knowledge to build a unifying view of the neuromodulation of different brain region
- Inform and attract new talent to drive forward neuromodulation research
- Inspire future directions that will transform our understanding of the neuromodulation of brain function and dysfunction and therapeutic intervention
- The NM² Conference will also provide a unique platform for students and junior researchers to interact with leaders in the field to collectively take part in shaping the future course of neuromodulatory research. Students and postdocs attending the event are invited to submit abstracts during registration to present a poster at the Conference.
Conference Host and Blue Brain Senior Scientist, Srikanth Ramaswamy is greatly looking forward to the event; “The NM² Conference will bring together researchers to bridge a variety of disciplines using state-of-the-art techniques in different brain regions towards the common goal of understanding the mechanisms and principles of neuromodulation.”
Founder and Director of the Blue Brain Project, Prof. Henry Markram commented; “The NM² Conference is designed to foster cross-disciplinary collaborations that will pave the way to enable the next breakthroughs in understanding the neuromodulatory control of brain states. We look forward to welcoming all conference speakers and participants.”
The first two days of the Conference 18-19 September, are being held at the SwissTech Convention Center on the EPFL Campus in Lausanne, before the Conference moves on 20 September to the Headquarters of Blue Brain at the Campus Biotech in Geneva.
Comprehensive Morpho-Electrotonic Analysis Shows two Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex.
In a paper published today, a team of scientists led by the Blue Brain Project have used a sophisticated type of mathematics in a way that it has never been used before in neuroscience.The team have uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.
This research, published in Frontiers in Computational Neuroscience, has significant implications for our understanding of the brain.
Rich cell-type-specific network topology in neocortical microcircuitry
Uncovering structural regularities and architectural topologies of cortical circuitry is vital for understanding neural computations.
In a paper published in Nature Neuroscience, the group of Idan Segev of the Hebrew University of Jerusalem in collaboration with the Cells & Circuits team in the Simulation Neuroscience Division of the Blue Brain, and Tel Aviv University identified a rich cell-type-specific network topology in neocortical microcircuitry. The systematic approach presented in the paper has enabled interpretation of microconnectomics ‘big data’, and provided several experimentally testable predictions.
Click here to read the paper.
Blue Brain wins major award of supercomputing time from DOE
A Blue Brain team, led by Eilif Muller, has won a major award of supercomputing time, from the DOE’s prestigious Incite Leadership Computing Program. The award gives the team an unprecedented opportunity to simulate synaptic plasticity—the process through which brain activity shapes synaptic connections. The study – which will build on Blue Brain’s recently published reconstruction of neural microcircuitry – it will focus on the impact of plasticity on the detailed organization and functioning of neural networks. The results will provide insights, not just to neuroscientists but also to technologists, seeking to implement brain-like learning mechanisms in software and hardware.
Allen Brain Institute collaborates with Blue Brain Project to model neurons from mouse visual cortex
On, the US-based Allen Institute released a set of 40 computer models of neurons from the mouse visual cortex, created using tools developed by the Blue Brain Project. Using Blue Brain technology, the researchers were able to reproduce the physiology and electrical activity of the neurons with an extremely high level of detail. For further details click here.
Blue Brain Project releases Open Source Software providing model parameter optimization for neuroscientists
The Allen Brain Institute recently used Blue Brain modelling and optimization tools to model neurons from mouse visual cortex (see news below). Now other neuroscientists can use Blue Brain tools to optimize their own models. The Blue Brain Project has just released the BlueBrain Python Optimization Library (BluePyOpt) – an extensible open source framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. The library includes methods for setting up small- and large-scale optimizations on a broad range of compute platforms – from laptops to large cloud-based compute infrastructures. The code can be downloaded here. A preprint describing the library is available here.
The Blue Brain Project has announced the opening of the Neocortical Microcircuit Collaboration Portal (NMC-Portal). The NMC portal allows researchers with access to the Internet, to access the experimental data used in the reconstruction, to download cellular and synaptic models, and to analyze the predicted properties of the microcircuit It also provides data supporting comparison of the anatomy and physiology of the reconstructed microcircuit against results in the literature. The aim is to catalyse community efforts to understand the cellular and synaptic organization of neocortical microcircuitry (ion channels and their densities, neuron types and their distributions across layers, connectivity between neurons, synapse types, synaptic properties etc.).. Future periodic releases will incorporate results from these efforts. To read more about the portal click here. To access the portal itself click here.
A paper published today describes a mathematical algorithm that predicts the location of nearly 40 million synapses formed between the neurons in a small block of brain tissue about 100’000 times larger than has ever been analyzed with electron microscopy. The algorithm uses millions of times less experimental data than would normally be needed using purely experimental methods. The algorithm was developed as part of the Blue Brain Project’s mission to digitally reconstruct the biological detail of the brain and is a companion paper to the team’s paper on the Reconstruction and Simulation of Neocortical Microcircuitry.
Digitizing and Simulating Neural Tissue Reveals Mechanisms Underlying Diverse Brain States
The Blue Brain Project has completed a first draft computer reconstruction of a piece of the neocortex. The electrical behavior of the virtual brain tissue was simulated on supercomputers and found to match the behavior observed in a number of experiments on the brain. Further simulations revealed novel insights into the functioning of the neocortex. This first step towards the digital reconstruction and simulation of the brain is published in Cell.
The Blue Brain Project visualization team has recently published an article on the modeling and simulation of brain imaging with light sheet fluorescence microscope (LSFM) on a physically plausible basis. This model reflects the light propagation in the optical setup of the LSFM using Monte Carlo rendering taking into account the physics of geometric optics. It can accurately render synthetic optical sections that are comparable to realistic ones produced by the LSFM. This in silico LSFM will be potentially employed for validating the reconstructed tissue models from microscopic imaging stacks.
Blue Brain Team Selected to Participate in Argonne Early Science Programme
The Blue Brain Project’s High Performance Computing Team (HPC) has been selected by the Argonne Leadership Computing Facility (ALCF) to participate in the 2-year Theta Early Science Program. This program will target the porting and optimization at large scale of our CoreNeuron scientific application on ALCF next leadership-class supercomputer prototype, Theta. This opportunity will allow the HPC team developers to collaborate with Intel, Cray and ALCF HPC specialists to drive the development of CoreNeuron to support 4 challenging scientific use cases: (a) The analysis of the electrical activity of the mouse brain Somatosensory Cortex, (b) The study of Synaptic Plasticity phenomenon in a mouse brain, (c) The building and simulations of a full mouse brain model and (d) The study of the activity and plasticity of a mouse brain model when embedded into a simulated body interacting within its environment.
NEST User Workshop, 20-22 April 2015 in Geneva and Connectomics School, 9-16 May 2015, Florence.
EPFL and the Chinese Academy of Sciences will collaborate on Neuroinformatics platforms, Data and Knowledge integration, algorithms for Brain Reconstruction and Brain Atlas platforms.
Neurorobotics engineers from the Human Brain Project (HBP) have recently taken the first steps towards building a “virtual mouse” by placing a simplified computer model of the mouse brain into a virtual mouse body.
For all media enquiries, please contact Kate Mullins – Communications Manager
Un super-ordinateur permettant de simuler le cerveau d’une souris vient d’être créé
Grâce a lui, les chercheurs de l’EPFL pourront reproduire, en trois dimensions, les 70 millions de neurones d’un cerveau de souris >>.
For almost a century, scientists have been studying brain waves to learn about mental health and the way we think >>.
The organizers of the BMI Research Day are happy to announce the program of the 2nd BMI Research Day 2014. The event takes place on June 11th and will start at 11:50 in EPFL (SV1717A / SV Lobby).
For all media enquiries, please contact Kate Mullins – Communications Manager